:: DESCRIPTION
Redeem (Read error detection in repetitive genomes)detects sequencing errors in Illumina reads (might be applicable for other types of next-gen sequencing equipments).
::DEVELOPER
Prof. Srinivas Aluru Research group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
X. Yang, S. Aluru and K. Dorman,
“Repeat-aware Modeling and Correction of Short Read Errors”,
BMC Bioinformatics, 2011 to appear.
:: DESCRIPTION
Quake is a package to correct substitution sequencing errors in experiments with deep coverage (e.g. >15X), specifically intended for Illumina sequencing reads. Quake adopts the k-mer error correction framework, first introduced by the EULER genome assembly package. Unlike EULER and similar progams, Quake utilizes a robust mixture model of erroneous and genuine k-mer distributions to determine where errors are located. Then Quake uses read quality values and learns the nucleotide to nucleotide error rates to determine what types of errors are most likely. This leads to more corrections and greater accuracy, especially with respect to avoiding mis-corrections, which create false sequence unsimilar to anything in the original genome sequence from which the read was taken.
::DEVELOPER
Center for Computational Biology , Johns Hopkins University School of Medicine
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Genome Biology 2010, 11:R116
Quake: quality-aware detection and correction of sequencing errors
David R Kelley, Michael C Schatz and Steven L Salzberg
